Takemura left the room right before the murder happened, the only two people present were his Lord Saburo and the Son Yorinobu. The next time the player encounters Takemura is at the waste site, with him holding the fixer, that killed the player, hostage and executing him.
Takemura, now a Ronin with a vengeance, is there with two objects in mind: He wants to avenge his Lord's death, while having doubts about the circumstances. As Saburo's prime bodyguard and executioner, Takemura knew about the family power struggle and the divide between Father and Son.
The Fixer told Takemura that he killed us, the player. But instead of immediately killing the fixer or bringing him into Arasaka Tower, Takemura goes to the landfill to find "our" body to learn more. There aren't other Arasaka forces present, Takemura is purposefully on hiws own.
All while Yorinobu, the new Arasaka Lord, knows that it is wise to keep an eye on Takemura. At the time Takemura finds the player he isn't an outcast yet, at least not officially, but he is also investigating "privately" and not on his new Lord's order. It is not in Yorinobu's interest to have Takemura lead the investigation and so Yorinobu does what he has to do when Takemura starts digging to deep (literally). He outcasts Takemura and orders his death.
The Arasaka Assassins attacking Takemura and the player during the car ride confirm Takemura's suspicions: The son is behind the murder.
At least that's how I understood it. There is a lot for the player to put together, which is fine as "we" were dead and the world kept on turning without us.
Maybe I misremember something wrong though. That's always a possibility with me.
. Anyway it looks like it was inspired by the Yamaha MX 61.
